Table 4. List of stacked bases along with their trajectory averaged stacking energy and the percentage of frames the interaction was present.

Stacked bases	Average Coulomb energy (kcal/mol)	Average VDW energy (kcal/mol)	Average stacking energy (kcal/mol)	% of frames
G527/C528	−6.8±1.3	−5.5±0.5	−12.2±1.4	100%
C528/G529	−2.8±1.1	−3.9±0.5	−6.7±1.2	99%
C528/A533	6.8±0.9	−0.6±0.1	6.2±0.9	28%
G529/A533	2.3±0.3	−0.6±0.1	1.8±0.3	22%
A532/G1206	1.9 ±0.8	−1.1±0.5	0.8±0.9	85%
A532/A1055	15.1±2.6	−1.1±0.4	14.1±2.6	40%
A532/U1056	5.5±2.5	−0.9±0.3	4.7±2.5	22%
A533/C536	6.7±1.9	−5.7±0.6	0.9±2.0	77%

A nucleotide can show up several times because it may create alternative stacking interactions with different nucleotides.